Sequential Analysis of the Origin of the Human Immunodeficiency Virus

This example shows pairwise sequence alignment (PWSA). PWSA has multiple applications in bioinformatics, such as multiple sequence analysis and phylogenetic tree reconstruction. We look at a PWSA that uses a global dynamic programming algorithm to align each pair of sequences, and we then calculate the pairwise distances using the Tajima-Nei metric. This gives us a matrix of distances between sequences that we use for inferring the phylogeny of HIV and SIV viruses. PWSA is a computationally expensive task with complexity O(L*L*N*N), where L is the average length of the sequences and N is the number of sequences [Durbin, et al. Cambridge University Press, 1998].